University of Hawaii at Manoa

About: University of Hawaii at Manoa is a education organization based out in Honolulu, Hawaii, United States. It is known for research contribution in the topics: Population & Sea surface temperature. The organization has 13693 authors who have published 25161 publications receiving 1023924 citations.

Assembling the marine metagenome, one cell at a time.

Abstract: The difficulty associated with the cultivation of most microorganisms and the complexity of natural microbial assemblages, such as marine plankton or human microbiome, hinder genome reconstruction of representative taxa using cultivation or metagenomic approaches. Here we used an alternative, single cell sequencing approach to obtain high-quality genome assemblies of two uncultured, numerically significant marine microorganisms. We employed fluorescence-activated cell sorting and multiple displacement amplification to obtain hundreds of micrograms of genomic DNA from individual, uncultured cells of two marine flavobacteria from the Gulf of Maine that were phylogenetically distant from existing cultured strains. Shotgun sequencing and genome finishing yielded 1.9 Mbp in 17 contigs and 1.5 Mbp in 21 contigs for the two flavobacteria, with estimated genome recoveries of about 91% and 78%, respectively. Only 0.24% of the assembling sequences were contaminants and were removed from further analysis using rigorous quality control. In contrast to all cultured strains of marine flavobacteria, the two single cell genomes were excellent Global Ocean Sampling (GOS) metagenome fragment recruiters, demonstrating their numerical significance in the ocean. The geographic distribution of GOS recruits along the Northwest Atlantic coast coincided with ocean surface currents. Metabolic reconstruction indicated diverse potential energy sources, including biopolymer degradation, proteorhodopsin photometabolism, and hydrogen oxidation. Compared to cultured relatives, the two uncultured flavobacteria have small genome sizes, few non-coding nucleotides, and few paralogous genes, suggesting adaptations to narrow ecological niches. These features may have contributed to the abundance of the two taxa in specific regions of the ocean, and may have hindered their cultivation. We demonstrate the power of single cell DNA sequencing to generate reference genomes of uncultured taxa from a complex microbial community of marine bacterioplankton. A combination of single cell genomics and metagenomics enabled us to analyze the genome content, metabolic adaptations, and biogeography of these taxa.

From shock breakout to peak and beyond: Extensive panchromatic observations of the type Ib supernova 2008D associated with swift x-ray transient 080109

Abstract: We present extensive early photometric (ultraviolet through near-infrared) and spectroscopic (optical and near-infrared) data on supernova (SN) 2008D as well as X-ray data analysis on the associated Swift X-ray transient (XRT) 080109. Our data span a time range of 5 hr before the detection of the X-ray transient to 150days after its detection, and a detailed analysis allowed us to derive constraints on the nature of the SN and its progenitor; throughout we draw comparisons with results presented in the literature and find several key aspects that differ. We show that the X-ray spectrum of XRT 080109 can be fit equally well by an absorbed power law or a superposition of about equal parts of both power law and blackbody. Our data first established that SN 2008D is a spectroscopically normal SN Ib (i.e., showing conspicuous He lines) and showed that SN 2008D had a relatively long rise time of 18days and a modest optical peak luminosity. The early-time light curves of the SN are dominated by a cooling stellar envelope (for Δt0.1-4days, most pronounced in the blue bands) followed by 56Ni decay. We construct a reliable measurement of the bolometric output for this stripped-envelope SN, and, combined with estimates of E K and M ej from the literature, estimate the stellar radius R ⊙ of its probable Wolf-Rayet progenitor. According to the model of Waxman etal. and Chevalier & Fransson, we derive R W07⊙ = 1.2 0.7R ⊙ and R CF08⊙ = 12 7 R ⊙, respectively; the latter being more in line with typical WN stars. Spectra obtained at three and four months after maximum light show double-peaked oxygen lines that we associate with departures from spherical symmetry, as has been suggested for the inner ejecta of a number of SN Ib cores. © 2009. The American Astronomical Society. All rights reserved.

The Global Phosphorus Cycle

Abstract: Phosphorus is an essential nutrient for all life-forms It is a key player in fundamental biochemical reactions involving genetic material (DNA and RNA) and energy transfer (ATP) and in structural support of organisms provided by membranes (phospholipids) and bone (the biomineral hydroxyapatite) Photosynthetic organisms utilize dissolved phosphorus, carbon, and other essential nutrients to build their tissues using energy from the sun Biological productivity is contingent upon the availability of phosphorus to these simple organisms that constitute the base of the food web in both terrestrial and aquatic systems It begins with a brief overview of the various components of the global phosphorus cycle Estimates of the mass of important phosphorus reservoirs, transport rates (fluxes) between reservoirs Following the overview, various aspects of the global phosphorus cycle are examined in more depth, including a discussion of the most pressing research questions currently being posed and research efforts presently underway to address these questions

An Empirical Parameterization of Heterogeneous Ice Nucleation for Multiple Chemical Species of Aerosol

Abstract: A novel, flexible framework is proposed for parameterizing the heterogeneous nucleation of ice within clouds. It has empirically derived dependencies on the chemistry and surface area of multiple species of ice nucleus (IN) aerosols. Effects from variability in mean size, spectral width, and mass loading of aerosols are represented via their influences on surface area. The parameterization is intended for application in largescale atmospheric and cloud models that can predict 1) the supersaturation of water vapor, which requires a representation of vertical velocity on the cloud scale, and 2) concentrations of a variety of insoluble aerosol species. Observational data constraining the parameterization are principally from coincident field studies of IN activity and insoluble aerosol in the troposphere. The continuous flow diffusion chamber (CFDC) was deployed. Aerosol species are grouped by the parameterization into three basic types: dust and metallic compounds, inorganic black carbon, and insoluble organic aerosols. Further field observations inform the partitioning of measured IN concentrations among these basic groups of aerosol. The scarcity of heterogeneous nucleation, observed at humidities well below water saturation for warm subzero temperatures, is represented. Conventional and inside-out contact nucleation by IN is treated with a constant shift of their freezing temperatures. The empirical parameterization is described and compared with available field and laboratory observations and other schemes. Alternative schemes differ by up to five orders of magnitude in their freezing fractions (30°C). New knowledge from future observational advances may be easily assimilated into the scheme’s framework. The essence of this versatile framework is the use of data concerning atmospheric IN sampled directly from the troposphere.